(verb)

Definition: to penetrate into every part

source: http://www.merriam-webster.com/dictionary/honeycombed?show=0&t=1387316276

“Waterfront: A Walk Around Manhattan”:

“Three-quarters of the way across the bridge I saw the skyscrapers in the deepening darkness become slowly honeycombed with lights until, before I reach the Manhattan end…”

I understand where is the vantage point from author, how the darkness join to the light, the city become glorious.